Dear Jorge, For simplicity, I'd start with these two papers, both available on my webpage:
Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42:569–575. Theodore Garland, Jr., Paul H. Harvey, and Anthony R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18–32. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Jorge Sánchez Gutiérrez [jorgesgutier...@unex.es] Sent: Wednesday, August 20, 2014 9:49 AM To: r-sig-phylo@r-project.org Mailing-list Subject: [R-sig-phylo] multiple traits measured within species and populations Dear All, I'm working on some comparative analyses involving up to 312 populations of birds representing 112 species, one dependent variable (sometimes count data, e.g. species richness), various continuous independent variables (e.g. latitude, body mass), and a categorical variable (habitat: 3 levels). I'd be very grateful if I could get some input into these analyses: I constructed a phylogeny for the species in my data sets. Because some species had been examined in multiple study locations (up to 14), I represented these with multiple points and added them as polytomies to the appropriate species tip in the original tree (as in , e.g., Anderson et al.; Ecology Letters, (2005) 8: 310–318). This yielded an ultrametric tree containing multiple polytomies. I've been running regressions in APE using gls and the correlation structures implemented in the package and it seems to work well except for 'corPagel' when fitted with maximum likelihood (ML). In such a case I get the message: "Error in corFactor.corStruct(object) : NA/NaN/Inf in foreign function call (arg 1)". Example: m1 <- gls(richness ~ Mass + Habitat + Latitude, data= richness, correlation = CorPagel, method = "ML") But most importantly, I'm not sure if treating these points (means of 'populations') as statistically independent replicates is correct. I've read some papers regarding how to account for intraspecific variation in phylogenetic analyses (including those referred to in the 2nd edition of Paradis) and some related posts. However, as far as I know I think these methods account for between-individual variation instead of for between-population variation. In my data set the repeated observations per species do not correspond to different individuals but populations within species. Maybe I'm on the wrong track with this, so any help is very welcome. Best, Jorge Jorge S. Gutiérrez Department of Anatomy, Cell Biology & Zoology. Faculty of Sciences. University of Extremadura. Avenida de Elvas s/n. E-06006 Badajoz, Spain _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
